11-94406075-C-T

Variant names:

• chr11-94406075-C-T
• rs646130

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.661 in 151,950 control chromosomes in the GnomAD database, including 33,306 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.66 (33306 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.489

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.753 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.661 AC: 100297 AN: 151830 Hom.: 33281 Cov.: 31

Gnomad AFR AF: 0.640

Gnomad AMI AF: 0.403

Gnomad AMR AF: 0.673

Gnomad ASJ AF: 0.617

Gnomad EAS AF: 0.732

Gnomad SAS AF: 0.773

Gnomad FIN AF: 0.670

Gnomad MID AF: 0.725

Gnomad NFE AF: 0.661

Gnomad OTH AF: 0.673

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.661 AC: 100370 AN: 151950 Hom.: 33306 Cov.: 31 AF XY: 0.664 AC XY: 49313 AN XY: 74262

Gnomad4 AFR AF: 0.640

Gnomad4 AMR AF: 0.673

Gnomad4 ASJ AF: 0.617

Gnomad4 EAS AF: 0.731

Gnomad4 SAS AF: 0.774

Gnomad4 FIN AF: 0.670

Gnomad4 NFE AF: 0.660

Gnomad4 OTH AF: 0.666

Alfa AF: 0.642 Hom.: 5292

Bravo AF: 0.657

Asia WGS AF: 0.728 AC: 2530 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.48
DANN	Benign	0.63

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs646130; hg19: chr11-94139241;